Measuring disease similarity and predicting disease-related ncRNAs by a novel method

Background

Similar diseases are always caused by similar molecular origins, such as diasease-related protein-coding genes (PCGs). And the molecular associations reflect their similarity. Therefore, current methods for calculating disease similarity often utilized functional interactions of PCGs. Besides, the existing methods have neglected a fact that genes could also be associated in the gene functional network (GFN) based on intermediate nodes.

Methods

Here we presented a novel method, InfDisSim, to deduce the similarity of diseases. InfDisSim utilized the whole network based on random walk with damping to model the information flow. A benchmark set of similar disease pairs was employed to evaluate the performance of InfDisSim.

Results

The region beneath the receiver operating characteristic curve (AUC) was calculated to assess the performance. As a result, InfDisSim reaches a high AUC (0.9786) which indicates a very good performance. Furthermore, after calculating the disease similarity by the InfDisSim, we reconfirmed that similar diseases tend to have common therapeutic drugs (Pearson correlation γ²?=?0.1315, p?=?2.2e-16). Finally, the disease similarity computed by infDisSim was employed to construct a miRNA similarity network (MSN) and lncRNA similarity network (LSN), which were further exploited to predict potential associations of lncRNA-disease pairs and miRNA-disease pairs, respectively. High AUC (0.9893, 0.9007) based on leave-one-out cross validation shows that the LSN and MSN is very appropriate for predicting novel disease-related lncRNAs and miRNAs, respectively.

Conclusions

The high AUC based on benchmark data indicates the method performs well. The method is valuable in the prediction of disease-related lncRNAs and miRNAs.

     

二烯丙基二硫对荷S180肉瘤小鼠的辐射增敏效应

研究大蒜素重要活性成分二烯丙基二硫(Diallyl disulfide,DADS)对荷S180肉瘤小鼠的辐射增敏效应。利用X射线对荷瘤小鼠全身辐照。测量肿瘤体积、重量;检测肿瘤组织中细胞凋亡及Bcl-2、Bax、caspase-3等凋亡因子的表达。同时测定了DADS对S180细胞增殖及细胞内活性氧(reactive oxygen species,ROS)的影响。结果显示:与对照组、单纯药物组及单纯辐照组相比,DADS联合辐照组小鼠的肿瘤体变小、重量减轻(P<0.01);肿瘤组织中TUNEL阳性细胞增多(P<0.01);Bax、caspase-3表达增强,而Bcl-2表达减弱。此外,DADS引起了S180细胞内大量ROS的产生。结果提示DADS对荷S180肉瘤小鼠具有辐射增敏效应,其机制与上调Bax、Caspase-3、下调Bcl-2表达及诱导肿瘤细胞产生ROS有关。     

Proteomics analysis reveals diabetic kidney as a ketogenic organ in type 2 diabetes

Diabetic nephropathy (DN) is the leading cause of end-stage renal disease. To date, the molecular mechanisms of DN remain largely unclear. The present study aimed to identify and characterize novel proteins involved in the development of DN by a proteomic approach. Proteomic analysis revealed that 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase 2 (HMGCS2), the key enzyme in ketogenesis, was increased fourfold in the kidneys of type 2 diabetic db/db mice. Consistently, the activity of HMGCS2 in kidneys and 24-h urinary excretion of the ketone body β-hydroxybutyrate (β-HB) were significantly increased in db/db mice. Immunohistochemistry, immunofluorescence, and real-time PCR studies further demonstrated that HMGCS2 was highly expressed in renal glomeruli of db/db mice, with weak expression in the kidneys of control mice. Because filtered ketone bodies are mainly reabsorbed in the proximal tubules, we used RPTC cells, a rat proximal tubule cell line, to examine the effect of the increased level of ketone bodies. Treating cultured RPTC cells with 1 mM β-HB significantly induced transforming growth factor-β1 expression, with a marked increase in collagen I expression. β-HB treatment also resulted in a marked increase in vimentin protein expression and a significant reduction in E-cadherin protein levels, suggesting an enhanced epithelial-to-mesenchymal transition in RPTCs. Collectively, these findings demonstrate that diabetic kidneys exhibit excess ketogenic activity resulting from increased HMGCS2 expression. Enhanced ketone body production in the diabetic kidney may represent a novel mechanism involved in the pathogenesis of DN.     

p85alpha regulates osteoblast differentiation by cross-talking with the MAPK pathway

Class IA phosphoinositide 3-kinase (PI3K) is involved in regulating many cellular functions including cell growth, proliferation, cell survival, and differentiation. The p85 regulatory subunit is a critical component of the PI3K signaling pathway. Mesenchymal stem cells (MSC) are multipotent cells that can be differentiated into osteoblasts (OBs), adipocytes, and chondrocytes under defined culture conditions. To determine whether p85α subunit of PI3K affects biological functions of MSCs, bone marrow-derived wild type (WT) and p85α-deficient (p85α(-/-)) cells were employed in this study. Increased cell growth, higher proliferation rate and reduced number of senescent cells were observed in MSCs lacking p85α compare with WT MSCs as evaluated by CFU-F assay, thymidine incorporation assay, and β-galactosidase staining, respectively. These functional changes are associated with the increased cell cycle, increased expression of cyclin D, cyclin E, and reduced expression of p16 and p19 in p85α(-/-) MSCs. In addition, a time-dependent reduction in alkaline phosphatase (ALP) activity and osteocalcin mRNA expression was observed in p85α(-/-) MSCs compared with WT MSCs, suggesting impaired osteoblast differentiation due to p85α deficiency in MSCs. The impaired p85α(-/-) osteoblast differentiation was associated with increased activation of Akt and MAPK. Importantly, bone morphogenic protein 2 (BMP2) was able to intensify the differentiation of osteoblasts derived from WT MSCs, whereas this process was significantly impaired as a result of p85α deficiency. Addition of LY294002, a PI3K inhibitor, did not alter the differentiation of osteoblasts in either genotype. However, application of PD98059, a Mek/MAPK inhibitor, significantly enhanced osteoblast differentiation in WT and p85α(-/-) MSCs. These results suggest that p85α plays an essential role in osteoblast differentiation from MSCs by repressing the activation of MAPK pathway.     

高脂饲料诱导的肥胖大鼠网膜素水平的实验研究

人群调查发现肥胖人群网膜素水平较正常人群低,而正常及肥胖大鼠血清网膜素水平及其基因表达情况尚不清楚.将SD大鼠随机分为正常组(n=10)和高脂组(n=30),分别喂养普通饲料和高脂饲料.6 w后从高脂组选取体重增长最快的20只,再从中随机抽取10只继续喂养高脂饲料,12 w后两组各剩9只,采用全自动生化仪ADVIA2400测定血糖及血脂、ELISA检测血清胰岛素及网膜素水平、RT-PCR检测网膜脂肪组织网膜素mRNA表达水平.结果显示高脂组大鼠体重、体重增加值、肥胖指数、低密度脂蛋白、胰岛素、血清网膜素水平及网膜脂肪组织网膜素mRNA表达水平均高于正常组(P<0.05).首次发现肥胖大鼠血清网膜素水平及网膜脂肪组织中网膜素mRNA表达水平较正常大鼠显著增高,与人群调查结果不一致.     

云南哀牢山地区森林附生维管植物多样性及区系特征

附生植物作为山地森林生态系统中重要的结构性成分,在维持森林生态系统生物多样性格局、水分和养分循环等方面发挥着重要作用。本文通过野外调查、标本查阅并结合相关文献,对云南哀牢山地区附生维管植物物种组成及分布进行了系统研究。结果显示,哀牢山地区附生维管植物共有23科83属218种,其中附生蕨类和兰科植物最丰富。附生蕨类有34属93种,以附生-石生蕨类生活型占优势,其中水龙骨科17属62种,占附生蕨类的66.67%,瓦韦属(Lepisorus)和石韦属(Pyrrosia)分别有13种和10种。附生兰科植物有26属65种,其中石斛属(Dendrobium)和石豆兰属(Bulbophyllum)分别有12种和8种。该地区附生维管植物属的分布具有明显的热带性质并以热带亚洲分布居多。附生植物生长于生境因子变化剧烈、资源有限的林冠,对环境变化敏感,极易遭受破坏且破坏后难以恢复,不少附生植物具有很高的药用、观赏等价值。因此,应加强对附生维管植物这一特殊类群的保护。     

植物SUMO化修饰及其生物学功能

SUMO化修饰是细胞内蛋白质功能调节的重要方式之一。植物中的SUMO化修饰途径由SUMO分子和SUMO化酶系组成。SUMO化修饰是一个可逆的动态过程。SUMO前体蛋白在SUMO特异性蛋白酶的作用下成熟,随后通过SUMO活化酶、SUMO结合酶和SUMO连接酶将靶蛋白SUMO化,最后SUMO特异性蛋白酶将SUMO与靶蛋白分离,重新进入SUMO化循环。初步研究表明,植物SUMO化修饰参与植物花期调控、激素信号转导、抗病防御以及逆境应答等生理过程。     

Periplasmic proteins of Escherichia coli are highly resistant to aggregation: reappraisal for roles of molecular chaperones in periplasm

Periplasmic proteins of Gram-negative bacteria like Escherichia coli are subjected to immediate affect of environmental fluctuation that may unfold proteins, due to the permeability of the outer membrane to small molecules. They are thus supposedly protected by certain molecular chaperones. Nevertheless, no homologues of typical molecular chaperones have so far been found in periplasm, and the recently reported chaperone activities of periplasmic protein disulfide isomerase (PDI) and peptidyl prolyl isomerase (PPI) seem to be too weak to satisfy such assumed needs. In an attempt to reveal whether periplasmic proteins exhibit certain unusual properties, we discovered that such proteins as a whole are highly resistant to aggregation under a wide variety of denaturing conditions. Furthermore, in an effort to unveil the nature behind this phenomenon we purified and examined four prominent periplasmic proteins. Our results demonstrate that these proteins unfold at rather mild denaturing conditions and expose hydrophobic surfaces during such unfolding process, but hardly form complexes with a typical molecular chaperone. Based on these observations, we propose that the periplasmic proteins have been evolved to resist the formation of aggregates when subjected to various denaturing conditions and molecular chaperones may thus not be needed in periplasm.     

Soil respiration in Tibetan alpine grasslands: belowground biomass and soil moisture, but not soil temperature, best explain the large-scale patterns

The Tibetan Plateau is an essential area to study the potential feedback effects of soils to climate change due to the rapid rise in its air temperature in the past several decades and the large amounts of soil organic carbon (SOC) stocks, particularly in the permafrost. Yet it is one of the most under-investigated regions in soil respiration (Rs) studies. Here, Rs rates were measured at 42 sites in alpine grasslands (including alpine steppes and meadows) along a transect across the Tibetan Plateau during the peak growing season of 2006 and 2007 in order to test whether: (1) belowground biomass (BGB) is most closely related to spatial variation in Rs due to high root biomass density, and (2) soil temperature significantly influences spatial pattern of Rs owing to metabolic limitation from the low temperature in cold, high-altitude ecosystems. The average daily mean Rs of the alpine grasslands at peak growing season was 3.92 μmol CO(2) m(-2) s(-1), ranging from 0.39 to 12.88 μmol CO(2) m(-2) s(-1), with average daily mean Rs of 2.01 and 5.49 μmol CO(2) m(-2) s(-1) for steppes and meadows, respectively. By regression tree analysis, BGB, aboveground biomass (AGB), SOC, soil moisture (SM), and vegetation type were selected out of 15 variables examined, as the factors influencing large-scale variation in Rs. With a structural equation modelling approach, we found only BGB and SM had direct effects on Rs, while other factors indirectly affecting Rs through BGB or SM. Most (80%) of the variation in Rs could be attributed to the difference in BGB among sites. BGB and SM together accounted for the majority (82%) of spatial patterns of Rs. Our results only support the first hypothesis, suggesting that models incorporating BGB and SM can improve Rs estimation at regional scale.     

欧美杂种山杨体细胞无性系变异的分析

以成年欧美杂种山杨(Populustremula×P.tremuloides)优良无性系为材料,通过组织培养方法获得体细胞无性系,利用细胞学和分子生物学方法对其发生的变异进行研究。结果表明:用3.0mg.L-12,4-D诱导的再生植株的细胞染色体稳定性较差,所检测的144个细胞中,变异的细胞中多数发生了染色体加倍,二倍体细胞数仅占36.81%。有些染色体还发生了形态变异,染色体加长,形成带有随体或长臂较长的大型染色体。用1.0mg.L-16-BA诱导再生植株中染色体数量稳定性介于对照和3.0mg.L-12,4-D诱导的再生植株之间,在观察的142个细胞中二倍体细胞占54.93%。再生植株的AFLP分析表明,由激素诱导的再生植株中,AFLP谱带发生了变化,表明发生了体细胞无性系分子水平变异。